From the early history of rail transportation in the United States through the first half of the 20th century, New York City and Long Island were major areas for rail freight transportation. However, their relative isolation from the mainland United States has always posed problems for rail traffic. Numerous factors over the late 20th century have caused further declines in freight rail traffic. Efforts to reverse this trend are ongoing, but have been met with limited success.

The New York and Atlantic Railway currently operates all rail freight on the Long Island Rail Road (LIRR)'s rights-of-way on Long Island. CSX Transportation also operates within New York City, as do several shortline railroads including a car float across the harbor.

History

Early days

In part because of its easily accessible harbor and its canal connections to the interior, New York City and its surrounding area early on became the largest regional economy in North America. As railroads developed in the 19th century, serving New York City market was vital, but problematic. The Hudson River, a mile-wide (1.6 km) estuary near the city, a section also called the North River, presents a formidable barrier to rail transportation. As a result, most railroads terminated their routes at docks on the New Jersey shore (see 1900 map). Ferries brought rail passengers to and from the city, while car float barges carried freight cars across the Hudson—on the order of one million carloads of freight per year.

One exception was a New York Central Railroad line on the east bank of the Hudson that extended into Manhattan for freight service. The West Side Line, as it was called, brought freight cars to docks, warehouses and industries along Manhattan's west shore. Its southern portion included the High Line, a grade-separated viaduct that replaced the street-level railroad tracks on what was then known as "Death Avenue".

In the early 20th century, the Hudson barrier was surmounted by tunneling for passenger rail—and with the construction of the Holland Tunnel in 1927, the George Washington Bridge in 1931, and the Lincoln Tunnel in 1937—by creating fixed crossings for automobiles and trucks as well. Trucks could deliver freight anywhere in the city without requiring a railroad siding. The rail tunnels required electric propulsion, limiting their use for freight. A rail freight tunnel from Staten Island to Brooklyn was proposed, but never constructed.

Rail freight traffic east of the Hudson that did not cross by barge had to go north some distance to cross the river by bridge. The first rail crossing of the Hudson was the Poughkeepsie Bridge built in 1888. The New York Central crossed just south of Albany, New York, where it continued west paralleling the Erie Canal to create the Water Level Route which competed with the Pennsylvania Railroad's more direct route that had to cross the Allegany Mountains. Even though the Poughkeepsie Bridge was closer to the city, it was less used.

Post-World War II

The peak of rail freight came during World War II, when New York industries, including the Brooklyn Navy Yard, worked around the clock to support the war effort. After the war, the new Interstate Highway System, along with many inland waterways, both competed with the railroads. The rail industry went through widespread consolidations and bankruptcies. Containerization revolutionized shipping. The Port Authority developed the Port Newark-Elizabeth Marine Terminal on Newark Bay. Piers in Brooklyn and Manhattan lost traffic and were abandoned. The 1980 Staggers Rail Act largely deregulated the U.S. railroads. The railroads de-emphasized "retail" railroading—movement of one or a few rail cars from a shipper's siding to a destination siding—in favor of long unit trains for bulk commodities, such as coal and ore. General cargo shifted to intermodal movement, first trailer-on-flatcar (TOFC), intermodal containers on flat cars (COFC), and then double-stacked containers, loaded on special well cars. Much manufacturing shifted to Asia, particularly Japan and China, leading to a sharp increase in international container movements.

Industry developed highly efficient logistics based on strategically located distribution centers, often serving an entire metropolitan area with a single center. Goods in long distance containers, whether shipped by rail or sea, typically must be unpacked at a distribution center outside the city before being sent to an end destination, such as a retail store.

Heavy industry migrated out of the city. The Navy Yard closed in 1966. The Verrazzano–Narrows Bridge across the mouth of the harbor opened in 1964, allowing truck traffic to bypass Manhattan on the way to Long Island. The New York Central Railroad merged with the Pennsylvania Railroad to form the Penn Central in 1968, which then went bankrupt in 1970.Pinkston, Elizabeth (2003). "A Brief History of Amtrak." The Past and Future of U.S. Passenger Rail Service. (Washington, D.C.: U.S. Congressional Budget Office) The Poughkeepsie Bridge was closed after a fire in 1974 and has since been converted to a pedestrian and bicycle path. The 60th Street Yard in Manhattan was sold and redeveloped as the Riverside South apartment complex, while the 30th Street Yard was converted into the West Side Yard storage facility for Long Island Rail Road trains. The West Side Line was last used for freight in 1980. The below street level part North of the Pennsylvania Station was converted to passenger use as Amtrak's Empire Connection in 1991, with the portion south of Penn Station abandoned and later converted into the High Line, an elevated pedestrian park.

The numerous car float operations across New York Harbor shrank to a single cross harbor barge line, the New York Cross Harbor Railroad. It merged with a trucking company, then ran into financial difficulties and sold its cross harbor operation to New York New Jersey Rail, LLC, which was subsequently purchased by the Port Authority of New York and New Jersey.

Attempts to revive rail freight in the City and Long Island

Starting in the late 20th century, government officials have sought to increase the amount of freight to New York City and Long island that arrives by rail. To this end, several private and public sector initiatives have been undertaken: Construction of the Hunts Point Market in 1962, with extensive rail facilities connected to the Oak Point Yard The State of New York's $375 million "Full Freight Access Program" to allow cars with higher, TOFC clearance (but not double-stack) to reach Queens and Long Island, including construction of the Oak Point Link and the Harlem River Intermodal Yard in the Bronx. The link opened in 1998. The Harlem River Intermodal Yard was intended to handle intermodal containers but none were ever lifted there. Instead, it is being used for loading containerized trash onto trains for remote disposal. The restoration in 2006 of freight rail service to Staten Island via the Arthur Kill Vertical Lift Bridge at a cost of $72 million. The ExpressRail System, a $600 million investment in improved intermodal rail facilities at the container terminals on the west side of the Upper New York Bay and Newark Bay in New Jersey, and on Staten Island. The last yard of the project, next to Greenville yard, opened on January 7, 2019.Panynj Achieves Major Milestone in Efforts to Enhance Movement of Cargo by Rail Outside NY-NJ Region, Louanne Wong, Global Container Terminals, January 7, 2019 The grant of a concession in 1997 to a private short haul railroad, the New York and Atlantic Railway, to handle all rail freight on the Long Island Rail Road (LIRR)'s rights-of-way. The rebuilding of the 65th Street Yard, a rail yard at the Brooklyn shore with two car float bridges that allow rail cars to be loaded and unloaded onto barges, by the City and State in 1999 at a cost of $20 million.Operator Sought for Rebuilt Brooklyn Rail Yard, New York Times, August 31, 2000, Joseph Freed The car float bridges remained unused until 2012 because of financial disputes between the city and NYCHRR, which used bridges at the former Bush Terminal at 50th Street, instead. The 65th Street Yard was restored by the Port Authority for use by New York and New Jersey Rail, which it acquired in 2008. The use of $4.8 million of American Recovery and Reinvestment Act funds to rehabilitate an NY&A rail spur at Enterprise Park at Calverton (EPCAL), an industrial park located at Calverton, Long Island. The acquisition of the New York and New Jersey Rail cross harbor car float operations by the Port Authority in 2008 for $16 million. The Port Authority then acquired the New Jersey Greenville Yard in 2010 and awarded a contract for its reconstruction as a rail to barge facility in 2011. The authority's board authorized $118.1 million for the overall project. The State of New Jersey has budgeted $89 million in its 2012 budget to bring the Greenville Yard and Lift Bridge to a State-of-Good-Repair.FY 2012 Transportation Capital Program, New Jersey Department of Transportation The opening, in September 2011, of Brookhaven Rail Terminal (BRT), a privately financed $40 million, 28-acre transload facility. It is projected to take 40,000 trucks off Long Island roads and transfer 1 million tons of freight a year by 2016.Grand Opening of Brookhaven Freight Train Terminal , Carolyn Fortino, September 27, 2011 The terminal includes three tracks for construction material, such as lumber, asphalt and concrete, and six tracks for merchandise, such as flour and biodiesel. Plans to expand the yard have generated community opposition. Rehabilitation and reactivation of the South Brooklyn Marine Terminal (SBMT) along the Bay Ridge Channel in Sunset Park in late 2012. The terminal includes a 77-acre roll on/roll off automobile import and processing facility at the 39th Street pier, and an 11-acre, recycling facility for the city's plastic, metal and glass waste stream at the 30th Street pier. Both facilities are served by newly built rail connections to the 65th Street yard. Construction in 2014 of a transload facility for vegetable oil, food products and construction material at NYA's Wheel Spur Yard along Newtown Creek near Long Island City. NYA expects the facility to support replacement of the nearby Kosciuszko Bridge. The NYA also received permission from the LIRR, which owns most of the tracks on which NYA operates, to handle cars weighing up to , the top load limit for railroads in the eastern U.S. The previous LIRR limit was . New York City's 2006 municipal solid waste plan. Under the plan, most of the city's non-recyclable solid waste is placed in intermodal containers and transported by rail to disposal sites. Some of the containers are loaded onto rail cars in the city, while others are first moved across New York Harbor by barge to transfer stations in Staten Island and New Jersey.

Status

Routes As of late 2013, most rail freight to New York City moves over lines on the west side of the Hudson and is unloaded in New Jersey, where it is brought by truck to the city. Railroad freight cars that enter the city or Long Island do so via the Bronx, Brooklyn, or Staten Island.

The Bronx